![]() The count pipeline can take input from multiple sequencing runs on the same GEM well. It uses the Chromium cellular barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis. ![]() It is a wrapper around Illumina's bcl2fastq, with additional features that are specific to 10x Genomics libraries and a simplified sample sheet format.Ĭellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting. ![]() Cell Ranger includes five pipelines relevant to the 3' Single Cell Gene Expression Solutions and related products:Ĭellranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files. ![]() Cell Ranger7.1 (latest), printed on What is Cell Ranger?Ĭell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more (see list of example workflows and supported libraries).
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